Abstract: The pH value,total acid,non-volatile acid and amino acid of honey vinegar were determined,and the relationship between the quality of honey vinegar and honey vinegar strains was analyzed by metagenomic method.Through high throughput analysis,95.37% of 13490 Unigenes fragments could be annotated to NR database,97.1% of which belong to bacterial community. Komagataeibacter,Gluconobacter,Acetobacter,Gluconobacter and a small amount of Granulicella were the main genera of the microbial flora.A total of 12374(91.73%)ORFs were compared to KEGG database,with 10 and 14 major carbohydrate and amino acid metabolic pathways respectively. In the quality analysis of honey vinegar,a total of 11 free amino acids were detected in the fermentation broth,with pH value of 2.13,total acid of 33.5 g/L and non-volatile acid of 9.82 g/L.Further analysis of the relationship between several major functional microorganisms,metabolic pathways and vinegar quality showed that the flavor substances such as acetic acid,gluconic acid,butyric acid,aspartic acid,glutamic acid and the like were produced by the carbohydrate metabolism and amino acid metabolism pathways of Komagataeibacter xylinus,Komagataeibacter europaeus and gluconobacter sp. SXCC-1.This study provides theoretical basis for further optimizing the traditional Longmen honey vinegar process and stabilizing the product quality.